knitr/markdown: how to render math equations in vignettes built by CRAN?

Question

In a package, I have several vignettes that use mathematical notation, like:

This vignette illustrates the ideas behind solving systems of linear equations of the form $\mathbf{A x = b}$
where 

- $\mathbf{A}$ is an $m \times n$ matrix of coefficients for $m$ equations in $n$ unknowns
- $\mathbf{x}$ is an $n \times 1$ vector unknowns, $x_1, x_2, \dots x_n$
- $\mathbf{b}$ is an $m \times 1$ vector of constants, the "right-hand sides" of the equations

When I compile the vignette using R Studio (Ctrl+Shift+K), it renders properly in the HTML file, whether viewed in the R Studio viewer or the browser.

Yet, when the package is submitted to CRAN, and the vignettes are built there from the source package, the math is not rendered properly, but appears as markup,

Is there something I need to add to my YAML header so that vignettes built outside of R Studio will render mathematics properly? Currently, I use just a standard header:

---
title: "Solving Linear Equations"
author: "Me"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Solving Linear Equations}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

The generated pandoc command from R Studio is

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS linear-equations.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output pandoc8141d044063.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template "C:\R\R-3.2.5\library\rmarkdown\rmd\h\default.html" --css "C:\R\R-3.2.5\library\rmarkdown\rmarkdown\templates\html_vignette\resources\vignette.css" --mathjax --variable "mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --highlight-style pygments 

Perhaps I need to add a YAML option corresponding to --self-contained or --standalone ?

Answer 1

Posting years later in case another user has the same question. I noticed the same issues rendering equations in my vignettes---not on CRAN, just locally hosted packages. Ctrl + Shift + K rendered fine, but viewing with vignette() in the RStudio Help panel renders the equations badly.

I think this is just an issue that the Help panel doesn't render the HTML completely. If I view the packaged vignette in a browser, e.g. using RShowDoc(), then the equations are fine. So maybe users should be directed to RShowDoc() more often than vignette().